Chapter 6 Community composition
6.1 Taxonomy overview
6.1.1 Stacked barplot
genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
filter(count > 0) %>% #filter 0 counts
filter(!region %in% c("Eskoriatza","Villabona")) %>%
mutate(season=factor(season,levels=c("spring","autumn"))) %>%
ggplot(., aes(x=sample,y=count, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors) +
facet_nested(. ~ region + season, scales="free") + #facet per day and treatment
guides(fill = guide_legend(ncol = 1)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
axis.title.x = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black")) +
labs(fill="Phylum",y = "Relative abundance",x="Samples")
6.1.2 Phylum relative abundances
phylum_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
left_join(genome_metadata, by = join_by(genome == genome)) %>%
group_by(sample,phylum) %>%
summarise(relabun=sum(count))
phylum_summary %>%
group_by(phylum) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean) %>%
tt()| phylum | mean | sd |
|---|---|---|
| p__Bacteroidota | 5.343095e-01 | 0.2519907920 |
| p__Pseudomonadota | 1.645302e-01 | 0.2419531297 |
| p__Bacillota_A | 1.173726e-01 | 0.1119657856 |
| p__Verrucomicrobiota | 6.425495e-02 | 0.1307490386 |
| p__Bacillota | 3.864721e-02 | 0.0557437562 |
| p__Desulfobacterota | 2.040387e-02 | 0.0455321718 |
| p__Cyanobacteriota | 1.229173e-02 | 0.0511979549 |
| p__Chloroflexota | 9.260914e-03 | 0.0348103508 |
| p__Bacillota_C | 7.321975e-03 | 0.0141655787 |
| p__Fusobacteriota | 5.510315e-03 | 0.0138032117 |
| p__Acidobacteriota | 4.080066e-03 | 0.0190287052 |
| p__Myxococcota | 4.068355e-03 | 0.0400686546 |
| p__Deferribacterota | 3.293351e-03 | 0.0101979152 |
| p__Halobacteriota | 2.359186e-03 | 0.0198236928 |
| p__Planctomycetota | 2.008858e-03 | 0.0118013745 |
| p__Bacillota_B | 1.960581e-03 | 0.0031366435 |
| p__Patescibacteria | 1.911343e-03 | 0.0075513434 |
| p__Desulfobacterota_F | 1.150444e-03 | 0.0052791223 |
| p__Omnitrophota | 9.022635e-04 | 0.0055473998 |
| p__Spirochaetota | 7.487452e-04 | 0.0040145371 |
| p__Thermoproteota | 6.566364e-04 | 0.0024634359 |
| p__Methanobacteriota | 5.711150e-04 | 0.0038712346 |
| p__Campylobacterota | 5.678102e-04 | 0.0028643134 |
| p__ | 4.695129e-04 | 0.0039676126 |
| p__Fibrobacterota | 3.213383e-04 | 0.0031648149 |
| p__Actinomycetota | 3.002860e-04 | 0.0015353729 |
| p__Nanoarchaeota | 2.012785e-04 | 0.0017966105 |
| p__Desulfobacterota_G | 1.890416e-04 | 0.0015463557 |
| p__J088 | 1.850776e-04 | 0.0009813572 |
| p__Chlamydiota | 9.517468e-05 | 0.0004833040 |
| p__JAKLEM01 | 3.852292e-05 | 0.0003794068 |
| p__Iainarchaeota | 1.778707e-05 | 0.0001338011 |
phylum_arrange <- phylum_summary %>%
group_by(phylum) %>%
summarise(mean=mean(relabun)) %>%
arrange(-mean) %>%
select(phylum) %>%
pull()
phylum_summary %>%
filter(phylum %in% phylum_arrange) %>%
mutate(phylum=factor(phylum,levels=rev(phylum_arrange))) %>%
ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum)) +
scale_color_manual(values=phylum_colors[rev(phylum_arrange)]) +
geom_jitter(alpha=0.5) +
theme_minimal() +
theme(legend.position="none") +
labs(y="Phylum",x="Relative abundance")
6.2 Taxonomy boxplot
6.2.1 Family
family_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,family) %>%
summarise(relabun=sum(count))
family_summary %>%
group_by(family) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean) %>%
tt()| family | mean | sd |
|---|---|---|
| f__Bacteroidaceae | 2.102427e-01 | 1.955594e-01 |
| f__Rikenellaceae | 1.611894e-01 | 1.562459e-01 |
| f__Tannerellaceae | 7.299129e-02 | 6.664188e-02 |
| f__Aeromonadaceae | 5.225319e-02 | 1.358185e-01 |
| f__Akkermansiaceae | 4.800341e-02 | 1.226970e-01 |
| f__Marinifilaceae | 4.290443e-02 | 4.962259e-02 |
| f__Lachnospiraceae | 3.407472e-02 | 4.248629e-02 |
| f__Ruminococcaceae | 3.081005e-02 | 2.965309e-02 |
| f__Deianiraeaceae | 2.805932e-02 | 1.434462e-01 |
| f__Mycoplasmoidaceae | 2.649540e-02 | 4.798929e-02 |
| f__Enterobacteriaceae | 2.607933e-02 | 7.653830e-02 |
| f__ | 2.249364e-02 | 2.866260e-02 |
| f__Clostridiaceae | 1.941957e-02 | 4.169059e-02 |
| f__Chromatiaceae | 1.597569e-02 | 6.719385e-02 |
| f__Desulfovibrionaceae | 1.448492e-02 | 1.705853e-02 |
| f__Erysipelotrichaceae | 1.104908e-02 | 1.821438e-02 |
| f__Butyricicoccaceae | 9.720683e-03 | 4.494263e-02 |
| f__Diplorickettsiaceae | 8.263333e-03 | 7.249115e-02 |
| f__Chlorobiaceae | 8.082269e-03 | 5.368685e-02 |
| f__CAIVKH01 | 6.960373e-03 | 4.385676e-02 |
| f__Chromobacteriaceae | 5.687977e-03 | 3.831936e-02 |
| f__Fusobacteriaceae | 5.510315e-03 | 1.380321e-02 |
| f__Cellulosilyticaceae | 5.241853e-03 | 9.208240e-03 |
| f__VadinHA17 | 5.088929e-03 | 1.977358e-02 |
| f__P3 | 5.008918e-03 | 1.069121e-02 |
| f__FACHB-T130 | 4.282697e-03 | 4.152157e-02 |
| f__Smithellaceae | 4.231674e-03 | 3.872303e-02 |
| f__Oscillospiraceae | 4.122127e-03 | 4.776696e-03 |
| f__Polyangiaceae | 4.068355e-03 | 4.006865e-02 |
| f__SHND01 | 4.066311e-03 | 2.670163e-02 |
| f__CAG-239 | 3.660798e-03 | 6.287971e-03 |
| f__Chitinophagaceae | 3.547368e-03 | 1.671262e-02 |
| f__Rhodocyclaceae | 3.546631e-03 | 1.999856e-02 |
| f__Methylomonadaceae | 3.358104e-03 | 2.173751e-02 |
| f__Gastranaerophilaceae | 3.310922e-03 | 6.652166e-03 |
| f__Mucispirillaceae | 3.293351e-03 | 1.019792e-02 |
| f__Microcoleaceae | 3.259645e-03 | 2.029315e-02 |
| f__UBA6186 | 2.990942e-03 | 2.556453e-02 |
| f__EnvOPS12 | 2.866794e-03 | 9.720216e-03 |
| f__UBA11358 | 2.831247e-03 | 1.079693e-02 |
| f__Anaerovoracaceae | 2.355592e-03 | 2.819219e-03 |
| f__UBA1997 | 2.353806e-03 | 6.323583e-03 |
| f__Peptostreptococcaceae | 2.204895e-03 | 8.095665e-03 |
| f__Pumilibacteraceae | 2.190757e-03 | 6.124917e-03 |
| f__CHK158-818 | 2.050734e-03 | 3.904830e-03 |
| f__Peptococcaceae | 1.960581e-03 | 3.136644e-03 |
| f__Muribaculaceae | 1.944857e-03 | 3.177931e-03 |
| f__Methanotrichaceae | 1.861022e-03 | 1.802606e-02 |
| f__Burkholderiaceae_B | 1.860907e-03 | 8.600392e-03 |
| f__Methylococcaceae | 1.799044e-03 | 1.156777e-02 |
| f__Palsa-965 | 1.607561e-03 | 1.047557e-02 |
| f__Competibacteraceae | 1.594056e-03 | 1.515395e-02 |
| f__UBA3637 | 1.458445e-03 | 3.362239e-03 |
| f__Prolixibacteraceae | 1.429249e-03 | 6.122270e-03 |
| f__UBA5704 | 1.424231e-03 | 1.402705e-02 |
| f__B-1AR | 1.402641e-03 | 1.006339e-02 |
| f__Chloroflexaceae | 1.400177e-03 | 1.355414e-02 |
| f__Succinispiraceae | 1.397250e-03 | 2.545125e-03 |
| f__B-17BO | 1.328598e-03 | 8.384278e-03 |
| f__Microcystaceae_B | 1.272683e-03 | 1.173539e-02 |
| f__FEN-979 | 1.241677e-03 | 7.686017e-03 |
| f__Pirellulaceae | 1.154158e-03 | 9.332434e-03 |
| f__Massilibacillaceae | 1.109284e-03 | 5.877503e-03 |
| f__Methylophilaceae | 1.037785e-03 | 5.355410e-03 |
| f__Beijerinckiaceae | 1.035186e-03 | 4.457229e-03 |
| f__CAG-465 | 9.274101e-04 | 4.611188e-03 |
| f__Ignavibacteriaceae | 9.217538e-04 | 8.213255e-03 |
| f__Anaerotignaceae | 9.086293e-04 | 1.650081e-03 |
| f__Profunditerraquicolaceae | 9.022635e-04 | 5.547400e-03 |
| f__Pseudopelobacteraceae | 8.857441e-04 | 5.074400e-03 |
| f__UBA4417 | 8.455976e-04 | 5.163518e-03 |
| f__UBA5066 | 8.403140e-04 | 5.601038e-03 |
| f__UBA3700 | 8.067207e-04 | 2.729698e-03 |
| f__Pyrinomonadaceae | 7.220263e-04 | 5.094091e-03 |
| f__Opitutaceae | 7.101304e-04 | 6.993974e-03 |
| f__Victivallaceae | 7.026208e-04 | 3.743327e-03 |
| f__Thermoanaerobaculaceae | 6.814796e-04 | 6.711796e-03 |
| f__HGW-15 | 6.374558e-04 | 4.579831e-03 |
| f__4484-276 | 6.317310e-04 | 4.568187e-03 |
| f__Acutalibacteraceae | 6.098025e-04 | 4.563323e-03 |
| f__Paludibacteraceae | 5.835103e-04 | 5.070989e-03 |
| f__Methanobacteriaceae | 5.711150e-04 | 3.871235e-03 |
| f__UBA10030 | 5.519425e-04 | 3.031739e-03 |
| f__OLB5 | 5.252756e-04 | 3.582377e-03 |
| f__UBA3830 | 5.136412e-04 | 1.407875e-03 |
| f__F082 | 4.928572e-04 | 3.895817e-03 |
| f__Shewanellaceae | 4.927823e-04 | 2.267869e-03 |
| f__DYRC01 | 4.772738e-04 | 4.700602e-03 |
| f__Sedimentibacteraceae | 4.667661e-04 | 1.389224e-03 |
| f__JADJPG01 | 4.263615e-04 | 2.960895e-03 |
| f__UBA932 | 4.156228e-04 | 1.178640e-03 |
| f__Fen-1058 | 4.086113e-04 | 3.836266e-03 |
| f__Arcobacteraceae | 3.795084e-04 | 2.546493e-03 |
| f__UBA927 | 3.720772e-04 | 1.914678e-03 |
| f__Rectinemataceae | 3.564056e-04 | 3.510188e-03 |
| f__WRBN01 | 3.333468e-04 | 1.999495e-03 |
| f__GWF2-50-10 | 3.327121e-04 | 2.480457e-03 |
| f__Steroidobacteraceae | 3.265626e-04 | 2.177059e-03 |
| f__Hepatoplasmataceae | 2.940398e-04 | 2.271892e-03 |
| f__Planctomycetaceae | 2.891817e-04 | 2.848110e-03 |
| f__Methanocorpusculaceae | 2.866192e-04 | 1.094065e-03 |
| f__UBA4823 | 2.816756e-04 | 2.774183e-03 |
| f__Staskawiczbacteraceae | 2.657578e-04 | 2.400392e-03 |
| f__CAIRTM01 | 2.647003e-04 | 1.610403e-03 |
| f__UBA4778 | 2.605813e-04 | 1.471595e-03 |
| f__Coprobacillaceae | 2.512556e-04 | 7.367047e-04 |
| f__JAAUTT01 | 2.497687e-04 | 1.342951e-03 |
| f__Spirosomaceae | 2.470890e-04 | 1.347542e-03 |
| f__JAAYKM01 | 2.396380e-04 | 2.360160e-03 |
| f__UBA3254 | 2.373440e-04 | 1.827176e-03 |
| f__Gemmataceae | 2.328062e-04 | 2.292876e-03 |
| f__Saprospiraceae | 2.317820e-04 | 1.292124e-03 |
| f__UBA660 | 2.309557e-04 | 1.425198e-03 |
| f__Holophagaceae | 2.166536e-04 | 2.133790e-03 |
| f__UBA12108 | 2.154250e-04 | 1.514456e-03 |
| f__2-12-FULL-35-15 | 2.127537e-04 | 1.727718e-03 |
| f__Methanoregulaceae | 2.115446e-04 | 1.818352e-03 |
| f__GW2011-AR1 | 2.012785e-04 | 1.796610e-03 |
| f__Terrimicrobiaceae | 1.978209e-04 | 7.709831e-04 |
| f__Acidobacteriaceae | 1.953616e-04 | 1.924089e-03 |
| f__Syntrophorhabdaceae | 1.890416e-04 | 1.546356e-03 |
| f__UBA6016 | 1.883018e-04 | 1.303750e-03 |
| f__UBA3375 | 1.862708e-04 | 7.937741e-04 |
| f__Flavobacteriaceae | 1.829016e-04 | 1.620468e-03 |
| f__DUVY01 | 1.822525e-04 | 5.064739e-04 |
| f__SHXO01 | 1.797211e-04 | 8.927506e-04 |
| f__RUG14156 | 1.657852e-04 | 9.670025e-04 |
| f__UBA2023 | 1.651542e-04 | 1.140732e-03 |
| f__SPBP01 | 1.589463e-04 | 1.014813e-03 |
| f__LL51 | 1.572266e-04 | 9.059455e-04 |
| f__Crocinitomicaceae | 1.549871e-04 | 1.052732e-03 |
| f__2-12-FULL-60-25 | 1.541342e-04 | 1.081327e-03 |
| f__Lutisporaceae | 1.460459e-04 | 3.785647e-04 |
| f__Aestuariivirgaceae | 1.447142e-04 | 5.908593e-04 |
| f__Eubacteriaceae | 1.393410e-04 | 4.869468e-04 |
| f__SG8-41 | 1.297459e-04 | 9.992533e-04 |
| f__UBA9973 | 1.294228e-04 | 9.028722e-04 |
| f__UBA5976 | 1.252602e-04 | 7.247546e-04 |
| f__UBA1820 | 1.181123e-04 | 2.910814e-04 |
| f__Sphingomonadaceae | 1.152657e-04 | 5.446202e-04 |
| f__Absconditicoccaceae | 1.132011e-04 | 8.067896e-04 |
| f__Ilumatobacteraceae | 1.119473e-04 | 7.628420e-04 |
| f__TH1-2 | 1.094839e-04 | 6.706470e-04 |
| f__Rhabdochlamydiaceae | 9.517468e-05 | 4.833040e-04 |
| f__Amoebophilaceae | 9.033159e-05 | 5.611765e-04 |
| f__Mycoplasmataceae | 8.841740e-05 | 5.867263e-04 |
| f__Burkholderiaceae | 8.225897e-05 | 3.422233e-04 |
| f__JAGQMS01 | 7.555860e-05 | 3.616569e-04 |
| f__JAFDDL01 | 7.232997e-05 | 7.123676e-04 |
| f__Tenuifilaceae | 7.192224e-05 | 5.390355e-04 |
| f__Burkholderiaceae_A | 6.890317e-05 | 6.000937e-04 |
| f__Rhizobiaceae | 6.770667e-05 | 3.322745e-04 |
| f__UBA5272 | 6.344839e-05 | 5.321556e-04 |
| f__JAGOQP01 | 6.336248e-05 | 6.240480e-04 |
| f__Microbacteriaceae | 6.307851e-05 | 4.535380e-04 |
| f__SZUA-47 | 6.279603e-05 | 3.586105e-04 |
| f__Moraxellaceae | 5.992173e-05 | 4.649041e-04 |
| f__Brevinemataceae | 5.899281e-05 | 3.455812e-04 |
| f__CAG-508 | 5.239573e-05 | 3.378165e-04 |
| f__UBA1709 | 5.179159e-05 | 5.100880e-04 |
| f__UBA1568 | 4.952088e-05 | 2.986606e-04 |
| f__XYD1-FULL-46-19 | 4.915817e-05 | 4.354164e-04 |
| f__JAKLEM01 | 3.852292e-05 | 3.794068e-04 |
| f__CAIOMD01 | 3.103415e-05 | 1.937893e-04 |
| f__GWA2-36-10 | 2.884440e-05 | 2.345672e-04 |
| f__PALSA-1337 | 2.249398e-05 | 1.820714e-04 |
| f__UBA12049 | 1.906267e-05 | 1.685139e-04 |
| f__JAAZKV01 | 1.778707e-05 | 1.338011e-04 |
| f__Zambryskibacteraceae | 1.740558e-05 | 1.410053e-04 |
| f__UBA920 | 1.348493e-05 | 9.984023e-05 |
family_arrange <- family_summary %>%
group_by(family) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
select(family) %>%
pull()
# Per origin
family_summary %>%
left_join(genome_metadata %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors[-8]) +
geom_jitter(alpha=0.5) +
facet_grid(.~region)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
# Per season
family_summary %>%
left_join(genome_metadata %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors[-8]) +
geom_jitter(alpha=0.5) +
facet_grid(.~season)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
6.2.2 Genus
genus_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,phylum,genus) %>%
summarise(relabun=sum(count)) %>%
filter(genus != "g__") %>%
mutate(genus= sub("^g__", "", genus))
genus_summary_sort <- genus_summary %>%
group_by(genus) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean)
genus_summary_sort %>%
tt()| genus | mean | sd |
|---|---|---|
| Bacteroides | 2.046402e-01 | 1.953733e-01 |
| Mucinivorans | 9.924394e-02 | 1.365473e-01 |
| Parabacteroides | 6.237195e-02 | 5.788498e-02 |
| Aeromonas | 5.225319e-02 | 1.358185e-01 |
| CAJQOT01 | 2.805932e-02 | 1.434462e-01 |
| Odoribacter | 2.218113e-02 | 3.013106e-02 |
| Luteolibacter | 2.154040e-02 | 1.200740e-01 |
| Mycoplasma_L | 2.040488e-02 | 4.176073e-02 |
| Akkermansia | 1.792041e-02 | 3.645298e-02 |
| JADFUS01 | 1.681497e-02 | 1.658130e-02 |
| Rikenella | 1.564868e-02 | 2.937705e-02 |
| Clostridium | 1.199086e-02 | 2.212868e-02 |
| Thiodictyon | 1.147645e-02 | 4.824596e-02 |
| Parabacteroides_B | 1.010987e-02 | 1.489169e-02 |
| Hafnia | 9.663663e-03 | 3.830939e-02 |
| UBA866 | 9.264589e-03 | 1.479609e-02 |
| Aquirickettsiella | 8.263333e-03 | 7.249115e-02 |
| Sarcina | 7.428710e-03 | 2.241766e-02 |
| CAIVKH01 | 6.960373e-03 | 4.385676e-02 |
| SZUA-378 | 6.661372e-03 | 1.838064e-02 |
| Buttiauxella | 6.566993e-03 | 2.598993e-02 |
| Malacoplasma | 6.090519e-03 | 2.462978e-02 |
| Chlorobaculum | 5.395630e-03 | 3.800456e-02 |
| LD21 | 5.088929e-03 | 1.977358e-02 |
| Citrobacter | 4.984853e-03 | 4.796159e-02 |
| Clostridium_Q | 4.898432e-03 | 5.777642e-03 |
| Alistipes | 4.515880e-03 | 6.268518e-03 |
| Hydrogenoanaerobacterium | 4.388173e-03 | 9.024943e-03 |
| FACHB-831 | 4.282697e-03 | 4.152157e-02 |
| Vogesella | 4.209095e-03 | 3.678975e-02 |
| Smithella | 4.156714e-03 | 3.798709e-02 |
| SHND01 | 4.066311e-03 | 2.670163e-02 |
| OM05-12 | 3.832406e-03 | 7.079937e-03 |
| Angelakisella | 3.793239e-03 | 4.933497e-03 |
| Mobilisporobacter | 3.653987e-03 | 1.032287e-02 |
| Hungatella_A | 3.630470e-03 | 6.092968e-03 |
| RUG14305 | 3.311659e-03 | 4.971494e-03 |
| JAGNZR01 | 3.281321e-03 | 9.557152e-03 |
| Planktothrix | 3.259645e-03 | 2.029315e-02 |
| Tidjanibacter | 3.180993e-03 | 5.865598e-03 |
| UBA6186 | 2.990942e-03 | 2.556453e-02 |
| FEN-1139 | 2.985961e-03 | 2.940831e-02 |
| UMGS1251 | 2.826349e-03 | 4.504858e-03 |
| UBA4132 | 2.776893e-03 | 1.944849e-02 |
| Chlorobium | 2.686638e-03 | 1.735463e-02 |
| Butyribacter | 2.665450e-03 | 2.625164e-02 |
| Anaerorhabdus | 2.588275e-03 | 9.581133e-03 |
| Budvicia | 2.586054e-03 | 9.218207e-03 |
| Anaerotruncus | 2.560824e-03 | 3.945328e-03 |
| Dielma | 2.369700e-03 | 3.784755e-03 |
| Cetobacterium | 2.216413e-03 | 6.456951e-03 |
| Bilophila | 2.076060e-03 | 3.433354e-03 |
| HGM05232 | 1.944857e-03 | 3.177931e-03 |
| JJ008 | 1.922642e-03 | 1.060181e-02 |
| Gallalistipes | 1.872220e-03 | 5.691823e-03 |
| Methanothrix | 1.861022e-03 | 1.802606e-02 |
| Alistipes_A | 1.829938e-03 | 3.396041e-03 |
| Gallibacteroides | 1.761646e-03 | 3.783251e-03 |
| OLB14 | 1.748534e-03 | 7.893428e-03 |
| CAKVBE01 | 1.683165e-03 | 5.685339e-03 |
| GCA-2737665 | 1.607561e-03 | 1.047557e-02 |
| RXIV01 | 1.594056e-03 | 1.515395e-02 |
| Craterilacuibacter | 1.478882e-03 | 1.128967e-02 |
| FEN-1279 | 1.402641e-03 | 1.006339e-02 |
| Chloroploca | 1.400177e-03 | 1.355414e-02 |
| Avirikenella | 1.328205e-03 | 3.941073e-03 |
| FEN-979 | 1.241677e-03 | 7.686017e-03 |
| Intestinimonas | 1.237653e-03 | 2.071632e-03 |
| JADLHS01 | 1.230710e-03 | 7.499137e-03 |
| Aureliella | 1.154158e-03 | 9.332434e-03 |
| Amedibacillus | 1.048792e-03 | 3.272116e-03 |
| Lamprocystis | 1.048543e-03 | 4.898854e-03 |
| Methylocystis | 1.035186e-03 | 4.457229e-03 |
| Novimethylophilus | 9.868698e-04 | 5.353028e-03 |
| CAJGBR01 | 9.829659e-04 | 1.426779e-03 |
| UBA2475 | 9.743695e-04 | 6.097399e-03 |
| Edwardsiella | 9.489498e-04 | 3.070027e-03 |
| RGIG5057 | 9.274101e-04 | 4.611188e-03 |
| IGN3 | 9.217538e-04 | 8.213255e-03 |
| Phocea | 9.159914e-04 | 1.927484e-03 |
| Romboutsia_D | 8.946029e-04 | 1.950782e-03 |
| UMGS1202 | 8.728213e-04 | 1.804112e-03 |
| Romboutsia_A | 8.584861e-04 | 5.034388e-03 |
| UBA5066 | 8.403140e-04 | 5.601038e-03 |
| UBA11358 | 8.313474e-04 | 4.169886e-03 |
| CAIPUE01 | 8.191449e-04 | 2.427991e-03 |
| Ferruginibacter | 8.056303e-04 | 3.536915e-03 |
| Anaerovorax | 7.982578e-04 | 1.578540e-03 |
| Azonexus | 7.884278e-04 | 3.623383e-03 |
| JABFSR01 | 7.691890e-04 | 3.989412e-03 |
| JAGAJR01 | 7.650787e-04 | 1.550967e-03 |
| Ruthenibacterium | 7.410260e-04 | 2.767581e-03 |
| UBA12294 | 7.405956e-04 | 3.885705e-03 |
| OLB17 | 7.220263e-04 | 5.094091e-03 |
| Bacteroides_G | 7.161553e-04 | 3.813060e-03 |
| JADKHC01 | 7.101304e-04 | 6.993974e-03 |
| RGIG7389 | 6.985219e-04 | 1.404616e-03 |
| Spyradomonas | 6.922726e-04 | 2.236942e-03 |
| Aminipila | 6.825982e-04 | 9.886491e-04 |
| UBA7488 | 6.802755e-04 | 2.335154e-03 |
| Pseudoflavonifractor | 6.421531e-04 | 1.658772e-03 |
| Draconibacterium | 6.410029e-04 | 2.707084e-03 |
| Harryflintia | 6.363666e-04 | 1.746416e-03 |
| Evtepia | 6.322927e-04 | 1.259868e-03 |
| CAJATL01 | 6.317310e-04 | 4.568187e-03 |
| Rhodoferax_C | 6.305115e-04 | 4.874058e-03 |
| RGIG5270 | 6.160249e-04 | 3.441629e-03 |
| Methyloglobulus | 5.812108e-04 | 2.705964e-03 |
| UBA3961 | 5.724647e-04 | 2.628789e-03 |
| Methanobacterium_A | 5.711150e-04 | 3.871235e-03 |
| Anaerotignum | 5.595837e-04 | 1.290580e-03 |
| Bacilliculturomica | 5.428876e-04 | 1.259364e-03 |
| Robinsoniella | 5.385790e-04 | 2.056733e-03 |
| 14-2 | 5.263276e-04 | 2.565653e-03 |
| OLB5 | 5.252756e-04 | 3.582377e-03 |
| Hylemonella | 5.252227e-04 | 5.172844e-03 |
| Paludibacter | 5.231717e-04 | 5.042377e-03 |
| Scandinavium | 5.102891e-04 | 3.105545e-03 |
| JAERTD01 | 4.928572e-04 | 3.895817e-03 |
| Shewanella | 4.927823e-04 | 2.267869e-03 |
| DYRC01 | 4.772738e-04 | 4.700602e-03 |
| Copranaerobaculum | 4.711817e-04 | 1.711813e-03 |
| CAIPTY01 | 4.631029e-04 | 2.626182e-03 |
| Eubacterium_R | 4.598877e-04 | 4.529369e-03 |
| WRKB01 | 4.365612e-04 | 8.420634e-04 |
| JACRCG01 | 4.226413e-04 | 2.489191e-03 |
| SKHV01 | 4.204799e-04 | 4.141246e-03 |
| Egerieousia | 4.156228e-04 | 1.178640e-03 |
| JAGOBP01 | 4.086113e-04 | 3.836266e-03 |
| Limnohabitans | 4.058024e-04 | 2.403611e-03 |
| RPPU01 | 4.053898e-04 | 3.992626e-03 |
| JAKAJH01 | 3.996183e-04 | 2.723998e-03 |
| Aliarcobacter | 3.795084e-04 | 2.546493e-03 |
| UBA5195 | 3.776642e-04 | 2.283696e-03 |
| UBA6024 | 3.677665e-04 | 2.219403e-03 |
| JAJBUQ01 | 3.634658e-04 | 7.678166e-04 |
| UBA1306 | 3.564056e-04 | 3.510188e-03 |
| AM-1111 | 3.542287e-04 | 2.303794e-03 |
| Scatenecus | 3.470350e-04 | 1.621431e-03 |
| UBA1794 | 3.361116e-04 | 1.492346e-03 |
| JAHHUI01 | 3.333468e-04 | 1.999495e-03 |
| GWF2-50-10 | 3.327121e-04 | 2.480457e-03 |
| CADEED01 | 3.265626e-04 | 2.177059e-03 |
| CAZU01 | 3.230268e-04 | 1.502801e-03 |
| JAGPHI01 | 3.061219e-04 | 1.510001e-03 |
| UBA4417 | 2.893080e-04 | 2.849353e-03 |
| TH-plancto1 | 2.891817e-04 | 2.848110e-03 |
| JAAYQI01 | 2.884768e-04 | 1.172060e-03 |
| CALXSC01 | 2.872357e-04 | 1.380046e-03 |
| Methanocorpusculum | 2.866192e-04 | 1.094065e-03 |
| CAIQJJ01 | 2.816756e-04 | 2.774183e-03 |
| Massiliimalia | 2.770692e-04 | 1.158610e-03 |
| CALURL01 | 2.735772e-04 | 1.381541e-03 |
| Negativibacillus | 2.673534e-04 | 8.605906e-04 |
| CAIRTM01 | 2.647003e-04 | 1.610403e-03 |
| JAEUNJ01 | 2.643866e-04 | 1.186509e-03 |
| CAJLXD01 | 2.616752e-04 | 9.849718e-04 |
| UBA2192 | 2.605813e-04 | 1.471595e-03 |
| Coprobacillus | 2.512556e-04 | 7.367047e-04 |
| Plesiomonas | 2.510777e-04 | 2.472828e-03 |
| Leadbetterella | 2.470890e-04 | 1.347542e-03 |
| Lacibacter | 2.466315e-04 | 2.198721e-03 |
| JAAYKM01 | 2.396380e-04 | 2.360160e-03 |
| UBA3254 | 2.373440e-04 | 1.827176e-03 |
| WRDF01 | 2.355657e-04 | 7.059549e-04 |
| RGDT01 | 2.328062e-04 | 2.292876e-03 |
| JAHHTP01 | 2.321481e-04 | 7.443505e-04 |
| JAFGIC01 | 2.320661e-04 | 2.285586e-03 |
| M3007 | 2.317820e-04 | 1.292124e-03 |
| Serratia_A | 2.209635e-04 | 1.348450e-03 |
| Holophaga | 2.166536e-04 | 2.133790e-03 |
| CAJAUT01 | 2.154250e-04 | 1.514456e-03 |
| 2-12-FULL-35-15 | 2.127537e-04 | 1.727718e-03 |
| Methanoregula | 2.115446e-04 | 1.818352e-03 |
| CAIQQL01 | 2.012785e-04 | 1.796610e-03 |
| Terracidiphilus | 1.953616e-04 | 1.924089e-03 |
| Syntrophorhabdus | 1.890416e-04 | 1.546356e-03 |
| Flavobacterium | 1.829016e-04 | 1.620468e-03 |
| UBA5026 | 1.821910e-04 | 1.348509e-03 |
| Rahnella | 1.803689e-04 | 1.253661e-03 |
| SHXO01 | 1.797211e-04 | 8.927506e-04 |
| CHH4-2 | 1.708571e-04 | 4.697032e-04 |
| Morganella | 1.661144e-04 | 1.371676e-03 |
| Sulfuritalea | 1.582309e-04 | 8.944958e-04 |
| IOR16 | 1.569932e-04 | 3.560310e-04 |
| Hespellia | 1.564312e-04 | 8.181518e-04 |
| M0103 | 1.549871e-04 | 1.052732e-03 |
| MWCR01 | 1.541342e-04 | 1.081327e-03 |
| JACRFF01 | 1.523242e-04 | 7.683019e-04 |
| Avimicrobium | 1.513856e-04 | 3.128958e-04 |
| Rhodoferax | 1.497042e-04 | 1.117247e-03 |
| Aestuariivirga | 1.447142e-04 | 5.908593e-04 |
| PALSA-1004 | 1.297459e-04 | 9.992533e-04 |
| Intestinibacillus | 1.212242e-04 | 4.281023e-04 |
| Aquisediminimonas | 1.152657e-04 | 5.446202e-04 |
| UBA668 | 1.119473e-04 | 7.628420e-04 |
| Vitreimonas | 1.094839e-04 | 6.706470e-04 |
| Fluviibacter | 1.058202e-04 | 3.751332e-04 |
| JAGOMW01 | 1.026608e-04 | 7.766701e-04 |
| PALSA-1444 | 9.517468e-05 | 4.833040e-04 |
| Merdenecus | 9.435047e-05 | 3.854333e-04 |
| Massilioclostridium | 9.062086e-05 | 2.962613e-04 |
| Cardinium | 9.033159e-05 | 5.611765e-04 |
| UBA9973 | 8.917879e-05 | 8.783093e-04 |
| Polynucleobacter | 8.225897e-05 | 3.422233e-04 |
| RGIG4140 | 8.096121e-05 | 5.359455e-04 |
| UBA10108 | 7.929866e-05 | 7.810012e-04 |
| JAGQMS01 | 7.555860e-05 | 3.616569e-04 |
| Hepatoplasma | 7.517161e-05 | 7.403545e-04 |
| JAJQEJ01 | 7.487018e-05 | 2.711640e-04 |
| Anaerobium | 7.329179e-05 | 2.450951e-04 |
| UBA8529 | 7.192224e-05 | 5.390355e-04 |
| JAAYCI01 | 7.014809e-05 | 2.914153e-04 |
| CAJBLF01 | 7.012992e-05 | 6.906996e-04 |
| MGBC133411 | 6.940542e-05 | 4.023300e-04 |
| JAEZVV01 | 6.890317e-05 | 6.000937e-04 |
| UBA11704 | 6.344839e-05 | 5.321556e-04 |
| RFTN01 | 6.279603e-05 | 3.586105e-04 |
| JAFGVL01 | 6.033861e-05 | 5.942663e-04 |
| Acinetobacter | 5.992173e-05 | 4.649041e-04 |
| RGIG8482 | 5.239573e-05 | 3.378165e-04 |
| Methylopumilus_A | 5.091526e-05 | 3.564476e-04 |
| HGM16780 | 5.028810e-05 | 2.219329e-04 |
| SSEF01 | 4.952088e-05 | 2.986606e-04 |
| JAKJEI01 | 4.915817e-05 | 4.354164e-04 |
| MGBC102946 | 4.876472e-05 | 4.802768e-04 |
| Lumbricidophila | 4.561574e-05 | 4.492630e-04 |
| Brevinema | 4.071840e-05 | 2.975509e-04 |
| UBA8515 | 4.024405e-05 | 2.258398e-04 |
| GWA2-36-10 | 2.884440e-05 | 2.345672e-04 |
| JACRJP01 | 2.249398e-05 | 1.820714e-04 |
| 2-01-FULL-39-10-A | 1.906267e-05 | 1.685139e-04 |
| JAAZKV01 | 1.778707e-05 | 1.338011e-04 |
| Aurantimicrobium | 1.746277e-05 | 7.395454e-05 |
| C7867-006 | 1.740558e-05 | 1.410053e-04 |
| Cetobacterium_A | 1.258077e-05 | 7.242913e-05 |
genus_arrange <- genus_summary %>%
group_by(genus) %>%
summarise(mean=sum(relabun)) %>%
filter(genus != "g__")%>%
arrange(-mean) %>%
select(genus) %>%
mutate(genus= sub("^g__", "", genus)) %>%
pull()
#Per pond
genus_summary %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
mutate(genus=factor(genus, levels=rev(genus_summary_sort %>% pull(genus)))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=genus, group=genus, color=phylum)) +
scale_color_manual(values=phylum_colors) +
geom_jitter(alpha=0.5) +
facet_grid(.~region)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")